Prediction of expected years of life using whole-genome markers

Abstract

Genetic factors are believed to account for 25% of the interindividual differences in Years of Life (YL) among humans. However, the genetic loci that have thus far been found to be associated with YL explain a very small proportion of the expected genetic variation in this trait, perhaps reflecting the complexity of the trait and the limitations of traditional association studies when applied to traits affected by a large number of small-effect genes. Using data from the Framingham Heart Study and statistical methods borrowed largely from the field of animal genetics (whole-genome prediction, WGP), we developed a WGP model for the study of YL and evaluated the extent to which thousands of genetic variants across the genome examined simultaneously can be used to predict interindividual differences in YL. We find that a sizable proportion of differences in YL-which were unexplained by age at entry, sex, smoking and BMI-can be accounted for and predicted using WGP methods. The contribution of genomic information to prediction accuracy was even higher than that of smoking and body mass index (BMI) combined; two predictors that are considered among the most important life-shortening factors. We evaluated the impacts of familial relationships and population structure (as described by the first two marker-derived principal components) and concluded that in our dataset population structure explained partially, but not fully the gains in prediction accuracy obtained with WGP. Further inspection of prediction accuracies by age at death indicated that most of the gains in predictive ability achieved with WGP were due to the increased accuracy of prediction of early mortality, perhaps reflecting the ability of WGP to capture differences in genetic risk to deadly diseases such as cancer, which are most often responsible for early mortality in our sample. © 2012 de los Campos et al.